Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate RR42_RS13355 RR42_RS13355 glutamyl-tRNA synthetase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__Cup4G11:RR42_RS13355 Length = 468 Score = 333 bits (854), Expect = 8e-96 Identities = 185/480 (38%), Positives = 280/480 (58%), Gaps = 24/480 (5%) Query: 5 VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64 VR R+APSPTG +H+GN R+AL+ + FAR G FI+R+EDTD +R+ + L + Sbjct: 6 VRTRFAPSPTGFIHLGNIRSALYPWAFARRMKGDFILRIEDTDVERSSQESVDVILEGMA 65 Query: 65 WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124 WL +D DE GP+ Q ER D Y+ +++L+ LAY CY + EEL+ R+ Q Sbjct: 66 WLDLDIDE--------GPFYQMERMDRYREVVKQMLDSELAYPCYMSTEELDALRDAQRE 117 Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAE---GRKPSIRFRVPEGKVIAFNDIVKGEISFESDG 181 RGE PRY+G R E K + G +P IRF+ P G + ++D VKG I +D Sbjct: 118 RGEKPRYNGFWRP----EPGKVLPAPPAGVQPVIRFKNPIGGSVVWDDAVKGRIEISNDE 173 Query: 182 IGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGH 241 + D VI + DGTPTYNF V IDD M++THV+RG+DH++NTP+QI I +A G P + H Sbjct: 174 LDDLVIARPDGTPTYNFCVVIDDLDMRITHVIRGDDHVNNTPRQINIIRALGGVAPVYAH 233 Query: 242 MTLIVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFI 301 + ++NE +K+SKR ++ + Y++ GYLPEA+ N++ LGW+ G+ E+F++EQF+ Sbjct: 234 LPTVLNEQGEKMSKRHGAMP--VTGYRDEGYLPEAVLNYLARLGWAH-GDAEIFSREQFV 290 Query: 302 EIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQE 361 E FD+ L KSPA ++ KL W+NN Y+K D ++ LT P ++ G E Sbjct: 291 EWFDLEHLGKSPAQYNPEKLAWLNNHYIKVGDNARLAGLTQPFIEALG------GKVEGA 344 Query: 362 WVRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPEVLSTFAAKLEEL 421 + +I L ++ + ++ + LF+ E + + KA + L A +L L Sbjct: 345 SLEGVIGLVKDRANTLKDVAQAALLFYRGEPQPDPALKAEHLNADILPALQALATRLAAL 404 Query: 422 EEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGKETAIQRLK 481 E+ + I A+ KAV E G K KL MP+R+ V GQ P + +EL G++T ++R++ Sbjct: 405 GEWKREEISAAFKAVLAEFGLKMPKLAMPVRLLVAGQLQTPAIDAVLELFGRDTVLRRIQ 464 Lambda K H 0.316 0.137 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 545 Number of extensions: 31 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 468 Length adjustment: 33 Effective length of query: 450 Effective length of database: 435 Effective search space: 195750 Effective search space used: 195750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory